rs12456880

Variant names:

• chr18-846743-T-C
• rs12456880

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.29 in 151,946 control chromosomes in the GnomAD database, including 7,200 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.29 (7200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43965 AN: 151830 Hom.: 7186 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.248

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.290 AC: 44023 AN: 151946 Hom.: 7200 Cov.: 32 AF XY: 0.292 AC XY: 21720 AN XY: 74274

African (AFR) AF: 0.403 AC: 16679 AN: 41382

American (AMR) AF: 0.351 AC: 5361 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 491 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2792 AN: 5176

South Asian (SAS) AF: 0.280 AC: 1344 AN: 4802

European-Finnish (FIN) AF: 0.224 AC: 2368 AN: 10574

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14232 AN: 67968

Other (OTH) AF: 0.248 AC: 524 AN: 2112

Alfa AF: 0.239 Hom.: 7506

Bravo AF: 0.304

Asia WGS AF: 0.384 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		0.052

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12456880; hg19: chr18-846744;